Computational Biology of Transcription Factor Binding
(Sprache: Englisch)
Authoritative and easy to use, this volume examines the computational analysis of the biological interpretations of transcription factor binding. Cutting-edge protocols for computer biologists are presented, in addition to tricks-of-the-trade from experts in the field.
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Authoritative and easy to use, this volume examines the computational analysis of the biological interpretations of transcription factor binding. Cutting-edge protocols for computer biologists are presented, in addition to tricks-of-the-trade from experts in the field.
Klappentext zu „Computational Biology of Transcription Factor Binding “
Transcriptional regulation controls the basic processes of life. Its complex, dynamic, and hierarchical networks control the momentary availability of messenger RNAs for protein synthesis. Transcriptional regulation is key to cell division, development, tissue differen- ation, and cancer as discussed in Chapters 1 and 2. We have witnessed rapid, major developments at the intersection of computational biology, experimental technology, and statistics. A decade ago, researches were struggling with notoriously challenging predictions of isolated binding sites from low-throughput experiments. Now we can accurately predict cis-regulatory modules, conserved cl- ters of binding sites (Chapters 13 and 15), partly based on high-throughput ch- matin immunoprecipitation experiments in which tens of millions of DNA segments are sequenced by massively parallel, next-generation sequencers (ChIP-seq, Chapters 9, 10, and 11). These spectacular developments have allowed for the genome-wide mappings of tens of thousands of transcription factor binding sites in yeast, bacteria, mammals, insects, worms, and plants. Please also note the no less spectacular failures in many laboratories around the world.
Through great experimental difficulty, we've witnessed rapid, crucial developments at the intersection of computational biology, experimental technology, and statistics through which the vital process of transcriptional regulation can be further examined. In Computational Biology of Transcription Factor Binding, experts in the field examine the basic principles and provide detailed guidance for the computational analyses and biological interpretations of transcription factor binding, while disclosing critical practical information and caveats that are missing from many research publications. The volume serves not only computational biologists but experimentalists as well, who may want to better understand how to design and execute experiments and to communicate more effectively with computational biologists, computer scientists, and statisticians. Written for the highly successful Methods in Molecular Biology(TM) series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results in the lab.
Authoritative and easy to use, Computational Biology of Transcription Factor Binding guides scientists working in this area and demands not only new experiments but also the re-annotation of existing experimental data and computational predictions leading to important ongoing, major paradigm changes for us all.
Authoritative and easy to use, Computational Biology of Transcription Factor Binding guides scientists working in this area and demands not only new experiments but also the re-annotation of existing experimental data and computational predictions leading to important ongoing, major paradigm changes for us all.
Inhaltsverzeichnis zu „Computational Biology of Transcription Factor Binding “
An Overview of the Computational Analyses and Discovery of Transcription Factor Binding Sites.- Components and Mechanisms of Regulation of Gene Expression.- Regulatory Regions in DNA: Promoters, Enhancers, Silencers, and Insulators.- Three-Dimensional Structures of DNA-Bound Transcriptional Regulators.- Identification of Promoter Regions and Regulatory Sites.- Motif Discovery Using Expectation Maximization and Gibbs' Sampling.- Probabilistic Approaches to Transcription Factor Binding Site Prediction.- The Motif Tool Assessment Platform (MTAP) for Sequence-Based Transcription Factor Binding Site Prediction Tools.- Computational Analysis of ChIP-seq Data.- Probabilistic Peak Calling and Controlling False Discovery Rate Estimations in Transcription Factor Binding Site Mapping from ChIP-seq.- Sequence Analysis of Chromatin Immunoprecipitation Data for Transcription Factors.- Inferring Protein-DNA Interaction Parameters from SELEX Experiments.- Kernel-Based Identification of Regulatory Modules.- Identification of Transcription Factor Binding Sites Derived from Transposable Element Sequences Using ChIP-seq.- Target Gene Identification via Nuclear Receptor Binding Site Prediction.- Computing Chromosome Conformation.- Large-Scale Identification and Analysis of C-Proteins.- Evolution of cis-Regulatory Sequences in Drosophila.- Regulating the Regulators: Modulators of Transcription Factor Activity.- Annotating the Regulatory Genome.- Computational Identification of Plant Transcription Factors and the Construction of the PlantTFDB Database.- Practical Computational Methods for Regulatory Genomics: A cisGRN-Lexicon and cisGRN-Browser for Gene Regulatory Networks.- Reconstructing Transcriptional Regulatory Networks Using Three-Way Mutual Information and Bayesian Networks.-Computational Methods for Analyzing Dynamic Regulatory Networks.
Bibliographische Angaben
- 2010, XI, 454 Seiten, Masse: 18 x 25,9 cm, Gebunden, Englisch
- Herausgegeben: Istvan Ladunga
- Verlag: Springer, Berlin
- ISBN-10: 1607618532
- ISBN-13: 9781607618539
Sprache:
Englisch
Rezension zu „Computational Biology of Transcription Factor Binding “
From the reviews:"Gives us an overview of transcription and its regulation. ... The methods are very up-to-date and clearly presented by authors ... . The use of tools for predicting transcription factors binding sites is also very carefully presented in a text that is accessible for beginners ... . In summary, this book presents an important tool for entering the growing field of bioinformatics and its use for the study of transcription. ... If we cannot read all books ever written, this one is a good choice." (Carla Columbano Oliveira, Brazilian Journal of Pharmaceutical Sciences, Vol. 47 (2), Summer, 2011)
Pressezitat
From the reviews:"Gives us an overview of transcription and its regulation. ... The methods are very up-to-date and clearly presented by authors ... . The use of tools for predicting transcription factors binding sites is also very carefully presented in a text that is accessible for beginners ... . In summary, this book presents an important tool for entering the growing field of bioinformatics and its use for the study of transcription. ... If we cannot read all books ever written, this one is a good choice." (Carla Columbano Oliveira, Brazilian Journal of Pharmaceutical Sciences, Vol. 47 (2), Summer, 2011)
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